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Sodium in PDB 6amh: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1):
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1), PDB code: 6amh was solved by A.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.756, 109.600, 160.882, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) (pdb code 6amh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1), PDB code: 6amh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:36.2
occ:1.00
 O A:HOH506 2.4 32.9 1.0
O A:HOH602 2.5 32.2 1.0
O A:TYR301 2.7 28.4 1.0
O A:GLY303 2.7 25.7 1.0
O A:SER263 2.9 28.1 1.0
OG A:SER263 3.2 29.0 1.0
OG A:SER265 3.3 28.7 1.0
O A:GLY227 3.6 21.7 1.0
C A:GLY303 3.8 26.7 1.0
O A:HOH574 3.9 20.6 1.0
C A:TYR301 3.9 28.9 1.0
C A:SER263 3.9 28.5 1.0
CB A:SER265 4.0 28.7 1.0
N A:GLY303 4.1 28.6 1.0
N A:SER265 4.3 29.0 1.0
CB A:SER263 4.3 29.1 1.0
C A:PRO302 4.3 29.8 1.0
C A:GLY227 4.3 21.0 1.0
CA A:GLY303 4.4 28.1 1.0
CA A:PRO302 4.6 30.1 1.0
CA A:SER263 4.6 29.0 1.0
N A:PRO302 4.7 29.9 1.0
CA A:GLY227 4.7 20.6 1.0
O A:PRO302 4.8 30.6 1.0
CA A:SER265 4.8 29.4 1.0
OE2 A:GLU251 4.8 24.8 1.0
N A:VAL304 4.8 26.2 1.0
O A:VAL226 4.9 21.1 1.0
CA A:TYR301 4.9 28.7 1.0
N A:ALA264 5.0 28.9 1.0

Sodium binding site 2 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:33.0
occ:1.00
 O B:TYR301 2.6 35.6 1.0
O B:HOH577 2.7 35.9 1.0
O B:GLY303 2.8 34.4 1.0
O B:SER263 2.9 39.7 1.0
OG B:SER265 3.0 40.2 1.0
OG B:SER263 3.1 39.7 1.0
O B:GLY227 3.7 29.4 1.0
CB B:SER265 3.8 40.2 1.0
C B:GLY303 3.8 35.2 1.0
C B:TYR301 3.9 36.0 1.0
C B:SER263 3.9 40.4 1.0
O B:HOH559 4.0 27.5 1.0
CB B:SER263 4.1 40.2 1.0
C B:PRO302 4.2 38.1 1.0
N B:GLY303 4.2 37.2 1.0
N B:SER265 4.3 40.8 1.0
C B:GLY227 4.4 28.8 1.0
O B:PRO302 4.4 38.9 1.0
CA B:GLY303 4.5 36.8 1.0
CA B:SER263 4.5 40.5 1.0
CA B:PRO302 4.6 38.2 1.0
CA B:SER265 4.7 41.0 1.0
N B:PRO302 4.7 37.3 1.0
CA B:GLY227 4.7 28.2 1.0
CA B:TYR301 4.8 35.0 1.0
OG B:SER292 4.8 61.6 1.0
OE2 B:GLU251 4.9 34.2 1.0
N B:VAL304 4.9 34.7 1.0
N B:TYR301 4.9 34.2 1.0
O B:VAL226 5.0 27.9 1.0
CB B:VAL304 5.0 33.5 1.0
CB B:TYR301 5.0 34.5 1.0

Sodium binding site 3 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:31.9
occ:1.00
 O C:HOH515 2.6 25.9 1.0
O C:TYR301 2.6 26.2 1.0
O C:HOH558 2.8 25.9 1.0
O C:GLY303 2.8 24.8 1.0
O C:SER263 2.8 27.4 1.0
OG C:SER263 3.1 28.6 1.0
OG C:SER265 3.1 28.1 1.0
C C:SER263 3.8 27.3 1.0
CB C:SER265 3.8 28.3 1.0
C C:TYR301 3.8 26.5 1.0
C C:GLY303 3.9 25.6 1.0
O C:GLY227 3.9 22.2 1.0
O C:HOH575 3.9 19.5 1.0
CB C:SER263 4.1 28.3 1.0
N C:GLY303 4.1 27.1 1.0
C C:PRO302 4.2 27.8 1.0
N C:SER265 4.2 28.1 1.0
CA C:SER263 4.4 27.6 1.0
CA C:PRO302 4.4 27.9 1.0
CA C:GLY303 4.4 26.8 1.0
C C:GLY227 4.5 21.9 1.0
O C:PRO302 4.6 28.7 1.0
N C:PRO302 4.6 27.5 1.0
CA C:SER265 4.7 28.4 1.0
OE2 C:GLU251 4.7 24.7 1.0
CA C:TYR301 4.9 26.1 1.0
N C:ALA264 4.9 27.3 1.0
N C:VAL304 4.9 25.5 1.0
CA C:GLY227 4.9 21.4 1.0

Sodium binding site 4 out of 4 in 6amh

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Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:29.9
occ:1.00
 O D:HOH560 2.4 35.7 1.0
O D:HOH594 2.5 29.8 1.0
O D:TYR301 2.6 30.5 1.0
O D:SER263 2.8 29.7 1.0
O D:GLY303 2.8 28.9 1.0
OG D:SER265 2.9 33.8 1.0
OG D:SER263 3.1 30.0 1.0
O D:GLY227 3.8 25.3 1.0
CB D:SER265 3.8 33.7 1.0
O D:HOH516 3.8 24.4 1.0
C D:TYR301 3.8 30.8 1.0
C D:SER263 3.9 30.4 1.0
C D:GLY303 3.9 29.6 1.0
CB D:SER263 4.0 29.9 1.0
C D:PRO302 4.2 31.5 1.0
N D:SER265 4.2 32.6 1.0
N D:GLY303 4.3 30.9 1.0
C D:GLY227 4.3 25.0 1.0
CA D:SER263 4.4 30.6 1.0
O D:PRO302 4.5 31.8 1.0
CA D:GLY303 4.5 30.6 1.0
CA D:PRO302 4.5 31.8 1.0
CA D:SER265 4.7 33.9 1.0
CA D:GLY227 4.7 24.5 1.0
N D:PRO302 4.7 31.6 1.0
CA D:TYR301 4.8 30.6 1.0
OE2 D:GLU251 4.8 26.8 1.0
OG D:SER292 4.9 33.6 1.0
N D:VAL304 4.9 29.5 1.0
CB D:TYR301 4.9 30.6 1.0
N D:TYR301 4.9 29.8 1.0
O D:VAL226 4.9 24.1 1.0
N D:ALA264 5.0 31.1 1.0

Reference:

A.R.Buller, P.Van Roye, J.K.B.Cahn, R.A.Scheele, M.Herger, F.H.Arnold. Directed Evolution Mimics Allosteric Activation By Stepwise Tuning of the Conformational Ensemble. J. Am. Chem. Soc. V. 140 7256 2018.
ISSN: ESSN 1520-5126
PubMed: 29712420
DOI: 10.1021/JACS.8B03490
Page generated: Tue Oct 8 01:51:18 2024

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